Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity.
Bottom Line: These suggest that the three aspects are genetically connected but the cause and effect relationships are still unknown.For example, physiologic TF binding studies involve many TFs, consequently, it is difficult to assign nucleosome reorganization to the binding site occupancy of any particular TF.Therefore, several aspects remain unclear: does TF binding influence nucleosome (re)organizations locally or impact the chromatin landscape at a more global level; are all or only a fraction of TF binding a result of reorganization in nucleosome occupancy and do all TF binding and associated changes in nucleosome occupancy result in altered gene expression?
Affiliation: GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India.Show MeSH
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Mentions: We next checked target-site nucleosome occupancy before and after NME2 induction (Figure 3A). On analyzing relative occurrence we found lower number of positioned nucleosomes in the vicinity (∼300–500 bp) of NME2 target sites in cells after NME2 induction (Figure 3B). Out of 3956 NME2 target sites (within −7.5 to +2.5 kb of TSS) unique to the NME2-induced cells, 1257 (31%) present on 1119 putative promoters were found to either overlap or were within 300 bases of a nucleosome in cells before NME2 induction. Furthermore, 870 (∼70%) of the 1257 sites were found to be nucleosome-free in the NME2-induced condition, which involved repositioning of 870 nucleosomes in 791 genes on NME2 induction. Together, these findings indicate that many of the NME2 binding sites occupied by nucleosomes in the un-induced condition in A549 cells became NME2-bound (and nucleosome-free) in the NME2-induced condition.
Affiliation: GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India.